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Abstract Background Solanum lycopersicum Linn. (Tomato, Family Solanaceae) is one of the fruits that are most consumed worldwide. The current research intends to emphasise the possibility of positive and therapeutic effects of S. lycopersicum seed extract (SLSE) on Alzheimer's disease's neurodegeneration effects being reversed in a study utilising rats exposed to aluminium chloride. Investigations were done on the cholinesterase and antioxidant in vitro activity of SLSE. Rats with Alzheimer's disease were given SLSE, and donepezil (500, and 10 mg/kg.b.wt., daily for six weeks, respectively) to test SLSE biological activity. Beam-balance and T-maze tests, as well as serum levels of AChE, norepinephrine, dopamine, serotonin, IL-6, glycated end product, BDNF, MDA, TAC, and GSH were assessed, accompanied with histological investigation. To impact the effectiveness of this extract, bioinformatics study was validated. Results Crude SLSE showed in vitro DPPH scavenging and AChE inhibition activities, indicating the extract might have anti-Alzheimer potential, which was validated using an aluminium-intoxicated rat model, in vivo. In Alzheimer's rats, in vivo studies showed considerable improvements, as seen by improved beam balance, and T-maze tests and decreased serum levels of AChE, norepinephrine, dopamine, serotonin, IL-6, glycated end product, BDNF, and MDA, with increasing in TAC, and GSH levels. Brain tissue histological tests revealed a largely typical pattern of collagen fibre distribution. LC–HRESIMS metabolomic profiling of crude SLSE identified 33 compounds. Furthermore, the bioinformatics study discovered 378 targets related to the major identified compounds, of which only 133 were related to Alzheimer's and memory disorders, with APP, AChE, and PSEN2 targets which were marked as the top genes. Gene enrichment analysis identified the arachidonic acid metabolism and PPAR signalling pathway as the biological pathways enriched by all the gene sets under investigation. Conclusion As a result, the study findings are expected to pave the way for the creation of dietary supplements for Alzheimer's disease management. Graphic abstract |